Inhibition of the transmembrane transporter ABCB1 overcomes resistance to doxorubicin in patient-derived organoid models of HCC.

BACKGROUND: Transarterial chemoembolization is the first-line treatment for intermediate-stage HCC. However, the response rate to transarterial chemoembolization varies, and the molecular mechanisms underlying variable responses are poorly understood. Patient-derived hepatocellular carcinoma organoids (HCCOs) offer a novel platform to investigate the molecular mechanisms underlying doxorubicin resistance. METHODS: We evaluated the effects of hypoxia and doxorubicin on cell viability and cell cycle distribution in 20 patient-derived HCCO lines. The determinants of doxorubicin response were identified by comparing the transcriptomes of sensitive to resistant HCCOs. Candidate genes were validated by pharmacological inhibition. RESULTS: Hypoxia reduced the proliferation of HCCOs and increased the number of cells in the G0/G1 phase of the cell cycle, while decreasing the number in the S phase. The IC50s of the doxorubicin response varied widely, from 29nM to >1µM. Doxorubicin and hypoxia did not exhibit synergistic effects but were additive in some HCCOs. Doxorubicin reduced the number of cells in the G0/G1 and S phases and increased the number in the G2 phase under both normoxia and hypoxia. Genes related to drug metabolism and export, most notably ABCB1, were differentially expressed between doxorubicin-resistant and doxorubicin-sensitive HCCOs. Small molecule inhibition of ABCB1 increased intracellular doxorubicin levels and decreased drug tolerance in resistant HCCOs. CONCLUSIONS: The inhibitory effects of doxorubicin treatment and hypoxia on HCCO proliferation are variable, suggesting an important role of tumor-cell intrinsic properties in doxorubicin resistance. ABCB1 is a determinant of doxorubicin response in HCCOs. Combination treatment of doxorubicin and ABCB1 inhibition may increase the response rate to transarterial chemoembolization.

Supervised learning based on tumor imaging and biopsy transcriptomics predicts response of hepatocellular carcinoma to transarterial chemoembolization.

Although transarterial chemoembolization (TACE) is the most widely used treatment for intermediate-stage, unresectable hepatocellular carcinoma (HCC), it is only effective in a subset of patients. In this study, we combine clinical, radiological, and genomics data in supervised machine-learning models toward the development of a clinically applicable predictive classifier of response to TACE in HCC patients. Our study consists of a discovery cohort of 33 tumors through which we identify predictive biomarkers, which are confirmed in a validation cohort. We find that radiological assessment of tumor area and several transcriptomic signatures, primarily the expression of FAM111B and HPRT1, are most predictive of response to TACE. Logistic regression decision support models consisting of tumor area and RNA-seq gene expression estimates for FAM111B and HPRT1 yield a predictive accuracy of ∼90%. Reverse transcription droplet digital PCR (RT-ddPCR) confirms these genes in combination with tumor area as a predictive classifier for response to TACE.

Response prediction of hepatocellular carcinoma undergoing transcatheter arterial chemoembolization: unlocking the potential of CT texture analysis through nested decision tree models.

OBJECTIVES: To investigate if nested multiparametric decision tree models based on tumor size and CT texture parameters from pre-therapeutic imaging can accurately predict hepatocellular carcinoma (HCC) lesion response to transcatheter arterial chemoembolization (TACE). MATERIALS AND METHODS: This retrospective study (January 2011-September 2017) included consecutive pre- and post-therapeutic dynamic CT scans of 37 patients with 92 biopsy-proven HCC lesions treated with drug-eluting bead TACE. Following manual segmentation of lesions according to modified Response Evaluation Criteria in Solid Tumors criteria on baseline arterial phase CT images, tumor size and quantitative texture parameters were extracted. HCCs were grouped into lesions undergoing primary TACE (VT-lesions) or repeated TACE (RT-lesions). Distinct multiparametric decision tree models to predict complete response (CR) and progressive disease (PD) for the two groups were generated. AUC and model accuracy were assessed. RESULTS: Thirty-eight of 72 VT-lesions (52.8%) and 8 of 20 RT-lesions (40%) achieved CR. Sixteen VT-lesions (22.2%) and 8 RT-lesions (40%) showed PD on follow-up imaging despite TACE treatment. Mean of positive pixels (MPP) was significantly higher in VT-lesions compared to RT-lesions (180.5 vs 92.8, p = 0.001). The highest AUC in ROC curve analysis and accuracy was observed for the prediction of CR in VT-lesions (AUC 0.96, positive predictive value 96.9%, accuracy 88.9%). Prediction of PD in VT-lesions (AUC 0.88, accuracy 80.6%), CR in RT-lesions (AUC 0.83, accuracy 75.0%), and PD in RT-lesions (AUC 0.86, accuracy 80.0%) was slightly inferior. CONCLUSIONS: Nested multiparametric decision tree models based on tumor heterogeneity and size can predict HCC lesion response to TACE treatment with high accuracy. They may be used as an additional criterion in the multidisciplinary treatment decision-making process. KEY POINTS: • HCC lesion response to TACE treatment can be predicted with high accuracy based on baseline tumor heterogeneity and size. • Complete response of HCC lesions undergoing primary TACE was correctly predicted with 88.9% accuracy and a positive predictive value of 96.9%. • Progressive disease was correctly predicted with 80.6% accuracy for lesions undergoing primary TACE and 80.0% accuracy for lesions undergoing repeated TACE.

Disruption of Coronin 1 Signaling in T Cells Promotes Allograft Tolerance while Maintaining Anti-Pathogen Immunity.

The ability of the immune system to discriminate self from non-self is essential for eradicating microbial pathogens but is also responsible for allograft rejection. Whether it is possible to selectively suppress alloresponses while maintaining anti-pathogen immunity remains unknown. We found that mice deficient in coronin 1, a regulator of naive T cell homeostasis, fully retained allografts while maintaining T cell-specific responses against microbial pathogens. Mechanistically, coronin 1-deficiency increased cyclic adenosine monophosphate (cAMP) concentrations to suppress allo-specific T cell responses. Costimulation induced on microbe-infected antigen presenting cells was able to overcome cAMP-mediated immunosuppression to maintain anti-pathogen immunity. In vivo pharmacological modulation of this pathway or a prior transfer of coronin 1-deficient T cells actively suppressed allograft rejection. These results define a coronin 1-dependent regulatory axis in T cells important for allograft rejection and suggest that modulation of this pathway may be a promising approach to achieve long-term acceptance of mismatched allografts.

Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking.

Histidine kinases are key components of regulatory networks in bacteria. Although many of these enzymes are bifunctional, mediating both phosphorylation and dephosphorylation of downstream targets, the molecular details of this central regulatory switch are unclear. We showed recently that the universal second messenger cyclic di-guanosine monophosphate (c-di-GMP) drives Caulobacter crescentus cell cycle progression by forcing the cell cycle kinase CckA from its default kinase into phosphatase mode. We use a combination of structure determination, modeling, and functional analysis to demonstrate that c-di-GMP reciprocally regulates the two antagonistic CckA activities through noncovalent cross-linking of the catalytic domain with the dimerization histidine phosphotransfer (DHp) domain. We demonstrate that both c-di-GMP and ADP (adenosine diphosphate) promote phosphatase activity and propose that c-di-GMP stabilizes the ADP-bound quaternary structure, which allows the receiver domain to access the dimeric DHp stem for dephosphorylation. In silico analyses predict that c-di-GMP control is widespread among bacterial histidine kinases, arguing that it can replace or modulate canonical transmembrane signaling.

Structural and biochemical investigation of two Arabidopsis shikimate kinases: the heat-inducible isoform is thermostable.

The expression of plant shikimate kinase (SK; EC 2.7.1.71), an intermediate step in the shikimate pathway to aromatic amino acid biosynthesis, is induced under specific conditions of environmental stress and developmental requirements in an isoform-specific manner. Despite their important physiological role, experimental structures of plant SKs have not been determined and the biochemical nature of plant SK regulation is unknown. The Arabidopsis thaliana genome encodes two SKs, AtSK1 and AtSK2. We demonstrate that AtSK2 is highly unstable and becomes inactivated at 37 °C whereas the heat-induced isoform, AtSK1, is thermostable and fully active under identical conditions at this temperature. We determined the crystal structure of AtSK2, the first SK structure from the plant kingdom, and conducted biophysical characterizations of both AtSK1 and AtSK2 towards understanding this mechanism of thermal regulation. The crystal structure of AtSK2 is generally conserved with bacterial SKs with the addition of a putative regulatory phosphorylation motif forming part of the adenosine triphosphate binding site. The heat-induced isoform, AtSK1, forms a homodimer in solution, the formation of which facilitates its relative thermostability compared to AtSK2. In silico analyses identified AtSK1 site variants that may contribute to AtSK1 stability. Our findings suggest that AtSK1 performs a unique function under heat stress conditions where AtSK2 could become inactivated. We discuss these findings in the context of regulating metabolic flux to competing downstream pathways through SK-mediated control of steady state concentrations of shikimate.